Physiological and transcriptomic analysis of purple flowering stalks (Brassica campestris var. purpurea) under cadmium stress and exogenous glutathione application.

Glutathione (GSH) has a beneficial effect on the response of plants to cadmium (Cd) stress. The physiological and molecular processes by which glutathione influences Cd tolerance in purple flowering stalks (a Brassica vegetable) remain unclear. The aim of this study was to investigate the role of exogenous GSH in alleviating Cd toxicity in purple flowering stalks.

Enhancing cryopreservation survival in Petunia × Calibrachoa 'Light Yellow' callus: Insights into material characteristics and genetic integrity.

Petunia × Calibrachoa 'Light Yellow' (× Petchoa 'Light Yellow') is a kind of perennial herbaceous flower obtained through intergeneric hybridization of Petunia and Calibrachoa with high ornamental value and wide application, facing challenges in seed acquisition. Expanding propagation through tissue culture is an economically efficient means. Hence, establishing an effective procedure for the storage of callus is essential for × Petchoa 'Light Yellow'.

Metabolomics Reveals Molecular Signatures for Psoriasis Biomarkers and Drug Targets Discovery.

Purpose: Psoriasis is a chronic, multi-system skin disease that can be influenced by immunological, environmental, and genetic factors. Plasma metabolomic analysis can provide a great deal of information on potential diagnostic biomarkers, pathogenesis and personalized treatment. However, the role of metabolites in psoriasis is unknown.

A systematic assessment of cell type deconvolution algorithms for DNA methylation data.

We performed systematic assessment of computational deconvolution methods that play an important role in the estimation of cell type proportions from bulk methylation data. The proposed framework methylDeConv (available as an R package) integrates several deconvolution methods for methylation profiles (Illumina HumanMethylation450 and MethylationEPIC arrays) and offers different cell-type-specific CpG selection to construct the extended reference library which incorporates the main immune cell subsets, epithelial cells and cell-free DNAs. We compared the performance of different deconvolution algorithms via simulations and benchmark datasets and further investigated the associations of the estimated cell type proportions to cancer therapy in breast cancer and subtypes in melanoma methylation case studies.

Efficacy of Donated Milk in Early Nutrition of Preterm Infants: A Meta-Analysis.

Background: Preterm birth is associated with an increased risk of many complications, which is a main public health problem worldwide with social and economic consequences. Human milk from breast feeding has been proved to be the optimal nutrition strategy for preterm infants when available. However, the lack of human milk from mothers makes formula widely used in clinical practice.

Efficacy of brachytherapy combined with endocrine therapy and external beam radiotherapy in the treatment of intermediate and high-risk localized prostate cancer.

Purpose: To explore the efficacy and safety of brachytherapy combined with endocrine therapy (ET) and external beam radiotherapy (EBRT) in the treatment of patients with intermediate- and high-risk localized prostate cancer (PCa).

Methods: A total of 128 patients with intermediate- and high-risk localized PCa treated in our hospital, were included, encompassing 64 cases undergoing brachytherapy combined with ET (control group), and 64 cases undergoing intensity-modulated EBRT on the above basis (combination group). The clinical efficacy, adverse reactions, the serum prostate specific antigen (PSA) level before and after treatment, maximum urinary flow rate (Qmax), and expanded prostate cancer index composite (EPIC) score were compared between the two groups.

Integrated Computational Pipeline for Single-Cell Genomic Profiling.

Purpose: Copy-number profiling of multiple individual cells from sparse sequencing may be used to reveal a detailed picture of genomic heterogeneity and clonal organization in a tissue biopsy specimen. We sought to provide a comprehensive computational pipeline for single-cell genomics, to facilitate adoption of this molecular technology for basic and translational research.

Materials And Methods: The pipeline comprises software tools programmed in Python and in R and depends on Bowtie, HISAT2, Matplotlib, and Qt.

Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing.

Copy number alterations (CNAs) play an important role in molding the genomes of breast cancers and have been shown to be clinically useful for prognostic and therapeutic purposes. However, our knowledge of intra-tumoral genetic heterogeneity of this important class of somatic alterations is limited. Here, using single-cell sequencing, we comprehensively map out the facets of copy number alteration heterogeneity in a cohort of breast cancer tumors.

methylDMV: SIMULTANEOUS DETECTION OF DIFFERENTIAL DNA METHYLATION AND VARIABILITY WITH CONFOUNDER ADJUSTMENT.

DNA methylation has emerged as promising epigenetic markers for disease diagnosis. Both the differential mean (DM) and differential variability (DV) in methylation have been shown to contribute to transcriptional aberration and disease pathogenesis. The presence of confounding factors in large scale EWAS may affect the methylation values and hamper accurate marker discovery.

Mammary Tumor-Associated RNAs Impact Tumor Cell Proliferation, Invasion, and Migration.

Long non-coding RNAs (lncRNAs) represent the largest and most diverse class of non-coding RNAs, comprising almost 16,000 currently annotated transcripts in human and 10,000 in mouse. Here, we investigated the role of lncRNAs in mammary tumors by performing RNA-seq on tumor sections and organoids derived from MMTV-PyMT and MMTV-Neu-NDL mice. We identified several hundred lncRNAs that were overexpressed compared to normal mammary epithelium.